This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Training Provided by Brendan MacLean on the Use of Skyline 1. Taught 3 hours of hands-on tutorials for CPTAC Verification Working Group Operators meeting at Broad Institute 2. Created 2 x 25 minute training videos for Skyline v0.5 3. Regular bimonthly instructional updates over WebEx for Verification Working Group 4. Regular WebEx sessions with Susan Abbatiello and Birgit Schilling, leaders of Verification Working Group 5. Multi-day site visit at Vanderbilt University, Liebler and Tabb labs 6. Presentation to Aebersold Lab in Zurich 7. Presentation at U. Zurich mini-symposium 8. Multi-day site visit at Broad Institute, Carr lab 9. Co-taught 1.5 hours of US HUPO quantitative proteomics course 10. Created 3 x 10-20 page tutorials in using Skyline v0.6 11. Answered 110 support requests on Skyline support board (many others through direct email) 12. WebEx sessions with Christina Ludwig of Aebersold Lab 13. Taught undergraduate Alana Killeen professional software development for independent study Training Provided by Jesse Canterbury on General Mass Spectrometry Analysis 1. Rob Moritz, Jeff Stevens (ISB): FAIMS, triple quad operation &data 2. interpretation 3. Matt Chambers (Vanderbilt): generating data files for unit tests of file reader code 4. Shawna Hengel (Med Chem, Goodlett): ECD experiments 5. Scott Shaffer (Med Chem, Goodlett): ion funnel &Velos troubleshooting 6. Jason Wooden (Puget Sound Blood Center): mass spec &HPLC operation 7. Katrina Claw (Swanson lab): mass spec operation 8. Jan Aagaard (Swanson lab): mass spec operation 9. Andrew Stergachis (Stamatoyannopoulos lab): mass spec operation 10. Sean McIlwain (Noble): DIA data interpretation 11. Mirela Andronescu (Noble): data conversion/interpretation Training Provided by Daniela Tomazela on General Mass Spectrometry Analysis 1. Michael Paulsen: (BChE) Skyline, Column Packing, Data Acquisition 2. Francisco Nociti Jr. (Cementum project) Sample Preparation: Tryptic Digestion, Data Acquisition, MSDaPl 3. Ling Wang (Baker Lab): Data Acquisition 4. Judit Marsillach (Furlong lab / OP Project): Tryptic Digestion, MCX Peptide Sample Cleanup, Column Packing 5. Andrew Stergachis (Stamatoyannopoulos lab): Skyline, MS Method setup, SRM data Analysis 6. Jason Wooden (Puget Sound Blood Center): Skyline, LTQ SRM data acquisition, SRM data analysis 7. Tomas Vaisar (Heinecke Lab): Scheduled SRM using Skyline Training Provided by Ed Hsieh on General Mass Spectrometry Analysis 1. Katrina Claw (Swanson Lab): packing capillary columns and use of Agilent 1100 HPLCs 2. Dao-Fu Dao (Rabinovitch Lab): packing capillary columns, with sample analysis on Waters nanoAcquity and Thermo LTQ-FT instruments and with data analysis. 3. Peter Straub (Vanderbilt): in data analysis with Bullseye. 4. Lea Starita (Fields Lab): in data analysis with Bullseye and capillary column packing. Training Provided by Gennifer Merrihew 1. MSDaPl / MacCoss lab pipeline help - Evvie Vincow, Lea Starita, Jan Aagard, Melody Rynerson, Katrina Claw, Renee George, Angela Poole 2. Orbitrap runs, sample prep discussions - Evvie Vincow, Lea Starita 3. GelFree - Lea Starita, Andrew Stergachis, Chuck Witkowski, Jeremy Norris 4. LTQ analysis help, column making help - Melody Rynerson, Katrina Claw, Renee George, Jan Aagard, Angela Poole, Lea Starita 5. Ancient Protein Sample Prep - Ben Novak, Tom Kaye, Matthew Fitzgibbon, Pavel Pezner, Martin McIntosh 6. Isotope labeling discussions - Soledad Undurraga 7. TAP-tagged FOXO cell lines - Matt Kaeberlein, Lara Shamieh